Commit f67d9fe6 authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

Check Directory Path in mkfastq

parent f513e97a
Pipeline #3917 failed with stages
in 51 seconds
......@@ -37,14 +37,7 @@ process checkDesignFile {
"""
hostname
ulimit -a
dL=`echo "$designLocation" | tr -d ' '`
if [ `dirname "$designLocation"` != `dirname "\$dL"` ]
then echo "Error: Spaces Found in Design Directory Path"
exit 5
elif [ `basename "$designLocation"` != `basename "\$dL"` ]
then mv "$designLocation" "\$dL"
fi
python3 "$baseDir/scripts/check_design.py" -d "\$dL"
python3 "$baseDir/scripts/check_design.py" -d "$designLocation"
"""
}
......@@ -67,19 +60,10 @@ process untarBCL {
"""
hostname
ulimit -a
tar_no=`echo "${tar}" | tr -d ' '`
if [ `dirname "${tar}"` != `dirname "\${tar_no}"` ]
then echo "Error: Spaces Found in BCL Directory Path"
exit 5
elif [ `basename "${tar}"` != `basename "\$dL"` ]
then mv "${tar}" "\${tar_no}"
fi
name=`echo ${tar} | rev | cut -f1 -d '.' | rev`;
if [ "\${name}" == "gz" ];
then tar -xvf "\$tar_no" -I pigz;
else tar -xvf "\$tar_no";
then tar -xvf "$tar" -I pigz;
else tar -xvf "$tar";
fi;
"""
}
......@@ -107,6 +91,19 @@ process mkfastq {
"""
hostname
ulimit -a
bcl_no=`readlink -e "${bcl}" | tr -d ' '`
if [ `dirname "${bcl}"` != `dirname "\${bcl_no}"` ]
then echo "Error: Spaces Found in BCL Directory Path"
exit 5
fi
dL=`readlink -e "$design" | tr -d ' '`
if [ `dirname "$design"` != `dirname "\$dL"` ]
then echo "Error: Spaces Found in Design Directory Path"
exit 5
fi
cellranger mkfastq --id="${bcl.baseName}" --run="$bcl" --csv=$design -r \$SLURM_CPUS_ON_NODE -p \$SLURM_CPUS_ON_NODE -w \$SLURM_CPUS_ON_NODE
"""
}
......
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